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MCCCS Towhee (OPLS-2001)

 

 

Overview
    This section covers the OPLS-2001 force field as it is implemented into the towhee_ff_OPLS-2001 file in the ForceFields directory. All of the Towhee atom types for the OPLS-2001 force field are listed, along with a short description of their meanings. For more information about the OPLS force fields see the Jorgensen group home page. Note that OPLS-2001 is a Lennard-Jones (12-6) force field and can only be combined with other Lennard-Jones (12-6) force fields. The rather famous OPLS water models are not included here as they are provided in their own force field files. Please see the TIP3P, TIP4P, and TIP5P web pages for more information about those water models. Note that OPLS-2001 was preceeded by a united-atom version of the force field called OPLS-ua and an earlier version of the all-atom force field called OPLS-aa. I would like to acknowledge W.L. Jorgensen for kindly providing me with an electronic copy of the OPLS-2001 parameters. Any discrepencies (especially typos) from the published OPLS-2001 force field values are the sole responsibility of Marcus G. Martin, and I welcome feedback on how this implementation compares with other programs.

     

References for OPLS-2001 OPLS-2001 in Towhee
    The official force field name for OPLS-2001 in Towhee is 'OPLS-2001'. Here I list all of the OPLS-2001 atom names for use in the towhee_input file, along with a brief description taken from the OPLS-2001 literature. Notice that OPLS-2001 uses almost the same naming conventions as the Amber param96 force field. This is not a coincedence as these force fields utilize many of the same bonded interaction terms. I have modified some of the atom names from the standard OPLS-2001 in order to create unique type names. This was needed because OPLS-2001 occasionally uses different bonded interactions for atoms which have the same atom name for nonbonded interactions. I do not always distinguish between the original OPLS-2001 comments, and my modifications as I have created several new atom names. Some of my comments are placed in [square brackets]. Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
      Bromine
    • 'Br-' : bromine ion (charge -1)[uses the parameters from the LGM force field]
    • Carbon
    • 'C a' : carbon in O-C=O acid
    • 'C k' : carbon in C=O not bonded to N, and not an acid group
    • 'C n' : carbon in N-C=O
    • 'C*' : aromatic C in 5-membered ring next to two carbons
    • 'CA~' : neutral aromatic carbon not at the junction of 5-membered and 6-membered rings
    • 'CA+' : aromatic carbon in guanidinium C+
    • 'CAj' : neutral aromatic carbon at the juction of 5-membered and 6-membered rings
    • 'CAxna' : special parameters for nucleotide bases. aromatic C in DAP C2,C3,C4 pyridine; Cytosine C4,C5,C6
    • 'CBxna' : special parameters for nucleotide bases. Adenine C4,C5,C6; Guanine C2,C4,C5
    • 'CB' : aromatic C at juntion of 5-membered and 6-membered rings
    • 'CKxna' : special parameters for nucleotide bases. Adenine C8 Guanine
    • 'C=' : alkene sp2 carbon (non-aromatic) interior carbons in a diene.
    • 'CM' : alkene sp2 carbon (non-aromatic)
    • 'CMxna' : special parameters for nucleotide bases. Carbon in Uracil C5,C6
    • 'CO' : sp3 anomeric carbon (bonded to ether O and alcohol O). this type shows up in carbohydrates
    • 'CQ' : sp2C in 6-membered ring between deprotonated N's
    • 'CR' : aromatic C in 5-membered ring next to two nitrogens
    • 'CS' : aromatic C which does not have 120 degree bond angles with all of its neighbors. Examples are C3 in pyrrole and C3 in furan
    • 'CT' : aliphatic sp3 hybrid carbon
    • 'CTf' : aliphatic sp3 hybrid carbon bonded to F (monoalkyl fluorides and perfluoroalkanes)
    • 'CTcf4' : aliphatic sp3 hybrid carbon bonded to F in CF4
    • 'CTxna' : special parameters for nucleotide bases. Thymine C-C5, 9-Me A or G C-N9
    • 'CU' : aromatic C which abuts NB in a heteroatom-heteroatom bond. Examples are C3 in pyrazole and C3 in isoxazole
    • 'CV' : aromatic C in 5-membered ring next to C and deprotonated N
    • 'CW' : sp2 aromatic C in 5-membered ring next to C and NH
    • Chlorine
    • 'Cl' : chlorine bonded to a carbon
    • 'Cl-' : chlorine ion (charge -1)
    • Fluorine
    • 'F' : fluorine nonionic (monoalkyl fluorides)
    • 'Fpf' : fluorine nonionic (perfluoroalkanes)
    • 'F-' : fluorine ion (charge -1)
    • Hydrogen
    • 'H' : H attached to N
    • 'H2xna' : special parameters for nucleotide bases. DAP H-amine, Cytosine, Adenine
    • 'HA' : H bonded to an aromatic ring
    • 'HC~1' : hydrogen attached to an sp3 carbon in most cases, see special cases of hydrogen below
    • 'HC~2' : H bonded to a non-aromatic sp2 carbon which is not bonded to a N, not double bonded to O, and is not bonded to C=O
    • 'HC~3' : H bonded to a C=O or bonded to a C which is bonded to a C=O
    • 'HC~4' : H bonded to a CT that is bonded to NT
    • 'HCxna' : special parameters for nucleotide bases. DAP H3,H4; Uracil H-C5,H-C6; Thymine H-CC5; Cytosine H-C5,H-C6; Adenine H-C2,H-C8; Guanine
    • 'HO' : H attached to O in alcohol
    • 'HS' : H attached to S
    • 'HW' : H on TIP3P, TIP4P or TIP5P water
    • Iodine
    • 'I-' : iodine ion (charge -1)
    • Lithium
    • 'Li+' : lithium ion (charge +1)
    • Nitrogen
    • 'N' : N in an amide
    • 'N2' : sp2 N of aromatic amines and guanidinium ions
    • 'NA' : sp2 aromatic N with H attached
    • 'NB' : sp2 N in 5-membered ring, deprotonated
    • 'NC' : sp2 N in 6-membered ring, deprotonated
    • 'NO' : sp2 N in a nitro group
    • 'NT~1' : sp3 N in ammonia
    • 'NT+1' : sp3 N in ammonium ion (charge +1)
    • 'NT~2' : sp3 N in primary, secondary, tertiary amine
    • 'NT+2' : sp3 N in primary, secondary, tertiary ammonium ion (charge +1)
    • Oxygen
    • 'O' : oxygen in C=O, not an acidic site
    • 'O2' : oxygen double bonded to carbon in COO- or COOH
    • 'OHa' : oxygen bonded to H in RCOOH
    • 'OHm' : oxygen bonded to H in a mono-alcohol
    • 'OHp' : oxygen bonded to H in polyols or phenol
    • 'OHd' : oxygen bonded to H in diols
    • 'OHt' : oxygen bonded to H in triols
    • 'OS' : sp3 O in an ether or acetal
    • 'OWt3p' : water oxygen in the TIP3P model
    • 'OWt4p' : water oxygen in the TIP4P model
    • 'OWt5p' : water oxygen in the TIP5P model
    • 'L4p' : negative charge site on the TIP4P water
    • 'L5p' : negative charge sites on the TIP5P water
    • Sodium
    • 'Na+' : sodium ion (charge +1)
    • Sulfur
    • 'S' : S in sulfide, disulfide
    • 'SH' : S in thiols
Coulombic interactions
    OPLS-2001 uses atom-centered point charges to represent the electrostatic interactions. I do not know of an automated way to assign these point charges. Instead, you need to consult the OPLS-2001 literature, or (even better) ask the Jorgensen group for a copy of the force field file, and then find molecules with similar moieties to the ones on the molecule you wish to simulate.
Improper torsions
    OPLS-2001 uses stereocenter improper torsions to enforce planarity in aromatic rings, around amide nitrogens, and around other sp2 carbons. Remember that you can set the improper type to 0 to have the code automatically determine the improper type (so long as inpstyle is 2).
Proteins
    OPLS-2001 has a complete parameter set for proteins, but I have not yet implemented this into the protein builder. It is on my list of things to do, but is not a high priority at the moment. If someone else would like to add it into the builder I would be happy to provide advice about how to perform that task. Note that since the OPLS-aa protein builder is implemented, only minor changes would be needed to implement OPLS 2001 (the primary difference is the amino-acid-specific torsions).
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Send comments to: Marcus G. Martin
Last updated: September 07, 2005